DOI: 10.5061/dryad.ttdz08m2x
title: Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri

description: Background Heligmosomoides bakeri (often mistaken for Heligmosomoides
 polygyrus) is a promising model for parasitic nematodes with the key
 advantage of being amenable to study and manipulation within a controlled
 laboratory environment. While draft genome sequences are available for
 this worm, which allow for comparative genomic analyses between nematodes,
 there is a notable lack of information on its gene expression. Methods We
 generated biologically replicated RNA-seq datasets from samples taken
 throughout the parasitic life of H. bakeri. RNA from tissue-dwelling and
 lumen-dwelling worms, collected under a dissection microscope, was
 sequenced on an Illumina platform. Results We find extensive
 transcriptional sexual dimorphism throughout the fourth larval and adult
 stages of this parasite and identify alternative splicing, glycosylation,
 and ubiquitination as particularly important processes for establishing
 and/or maintaining sex-specific gene expression in this species. We find
 sex-linked differences in transcription related to aging and oxidative and
 osmotic stress responses. We observe a starvation-like signature among
 transcripts whose expression is consistently upregulated in males, which
 may reflect a higher energy expenditure by male worms. We detect evidence
 of increased importance for anaerobic respiration among the adult worms,
 which coincides with the parasite’s migration into the physiologically
 hypoxic environment of the intestinal lumen. Furthermore, we hypothesize
 that oxygen concentration may be an important driver of the worms
 encysting in the intestinal mucosa as larvae, which not only fully exposes
 the worms to their host’s immune system but also shapes many of the
 interactions between the host and parasite. We find stage- and
 sex-specific variation in the expression of immunomodulatory genes and in
 anthelmintic targets. Conclusions We examine how different the male and
 female worms are at the molecular level and describe major developmental
 events that occur in the worm, which extend our understanding of the
 interactions between this parasite and its host. In addition to generating
 new hypotheses for follow-up experiments into the worm’s behavior,
 physiology, and metabolism, our datasets enable future more in-depth
 comparisons between nematodes to better define the utility of H. bakeri as
 a model for parasitic nematodes in general. 
description: Adult worms were removed from the intestinal tract day 10
 post-infection and isolated using a modified Baerman apparatus. They were
 washed three times with water and placed in Dulbecco’s modified eagle’s
 medium–high glucose (Sigma cat. D5796) where they were sexed and counted.
 Worms were either used immediately for feeding assays. Mixed sex groups of
 worms were incubated with or without beads ((108 beads per 5mL of media,
 Polysciences Inc., Cat. 18859-1for two days. Worms were euthanised with
 70% ethanol. Images were acquired using
 the Zeiss Axio ZoomV.16 stereoscopic microscope (Bio Core Facility,
 Department of Biological Sciences, University of Calgary). Brightfield and
 fluorescence images were taken either under the the PlanNeoFluar Z 1x/0.25
 FWD 56mm objective objective with the AxioCam High Resolution colour (HRc)
 and High-Resolution mono (HRm) cameras. Beads were counted manually by
 zooming into images by two independent observers.
description: # Bead feeding assay for *Heligmosomoides bakeri*: females vs males One
 Excel file (H.bakeri\_SPbulktranscriptomes\_xpn\_data) which contains all
 of the transcript expression data we generated in the study. 63 image
 files (TIF format) of the nematode *Heligmosomoides* bakeri. Male and
 female adult worms were fed beads to determine whether the rates of
 feeding differed between the sexes. Method: Adult worms were removed from
 the intestinal tract day 10 post-infection and isolated using a modified
 Baerman apparatus. They were washed three times with water and placed in
 Dulbecco’s modified eagle’s medium–high glucose (Sigma cat. D5796) where
 they were sexed and counted. Worms were either used immediately for
 feeding assays. Mixed sex groups of worms were incubated with or without
 beads ((108 beads per 5mL of media, Polysciences Inc., Cat. 18859-1for two
 days. Worms were euthanised with 70% ethanol. Images were acquired using
 the Zeiss Axio ZoomV.16 stereoscopic microscope (Bio Core Facility,
 Department of Biological Sciences, University of Calgary). Brightfield and
 fluorescence images were taken either under the PlanNeoFluar Z 1x/0.25 FWD
 56mm objective with the AxioCam High Resolution colour (HRc) and
 High-Resolution mono (HRm) cameras. Beads were counted manually by zooming
 into images by two independent observers. ## Description of the Data and
 file structure ### H.bakeri\_SPbulktranscriptomes\_xpn\_data The file
 contains four tabs. * The first tab is all the data, the following three
 are subsets that readers may find helpful. * In the first tab (All\_data),
 we give the following for each possible comparison for each transcript:
 TPM, baseMean, log2FoldChange, log-fold change standard error (lfcSE),
 stat, value, and adjusted p-value. * In the second tab (TPMs per sample),
 we give the TPMs for each comparison for each transcript. * In the third
 tab (TPMs means), we give the mean TPMs for each comparison for each
 transcript. * In the fourth tab (key stats), we give the log2FoldChange
 and adjusted p-value for each comparison for each transcript. Please note
 that researchers interested in finding the expression of their favourite
 gene(s) should use the fourth tab. It is important that you use the
 adjusted p-value (padj). We have only included the unadjusted p-value for
 the sake of completeness. If you wish to discuss this more, please email
 me jwasmuth@ucalgary.ca. ### Image files A zipped file that contains the
 image files (TIF format). The 'F' and 'M' in the file
 name denotes whether the nematode worm was female or male, respectively.
 The labels 'gfp' and 'bf' signify whether the image
 was taken under fluorescence or bright field, respectively. ##
 Sharing/access Information These data are part of a research paper
 investigating how *Heligmosomodies bakeri* develops inside its host:
 https://doi.org/10.1186/s13071-023-05785-2. The raw data have not been
 made available anywhere else.